metricTester (version 1.3.6)

runSimulations: Run defined spatial simulations

Description

Given a prepared simulations.input object, will run all specified spatial simulations, and return a list of randomized CDMs.

Usage

runSimulations(simulations.input, simulations, new_ = FALSE)

Arguments

simulations.input

Prepped simulations.input object

simulations

Optional. If not provided, defines the simulations as all of those in defineSimulations. If only a subset of those simulations is desired, then simulations should take the form of a character vector corresponding to named functions from defineSimulations. The available simulations can be determined by running names(defineSimulations()). Otherwise, if the user would like to define a new simulation on the fly, the argument simulations can take the form of a named list of new functions (simulations). In this case, new_ must be set to TRUE.

new_

Whether or not new simulations are being defined on the fly. Default is FALSE. Set to TRUE if a new metric is being used.

Value

A list of lists of simulation results, where each of the first-order elements in the list relates to a unique simulation as defined in defineSimulations.

Details

We ran three spatial simulations in our Ecography paper: neutral, habitat filtering, and competitive exclusion community assembly.

References

Miller, E. T., D. R. Farine, and C. H. Trisos. 2016. Phylogenetic community structure metrics and null models: a review with new methods and software. Ecography DOI: 10.1111/ecog.02070

Examples

# NOT RUN {
tree <- geiger::sim.bdtree(b=0.1, d=0, stop="taxa", n=50)

prepped <- prepSimulations(tree, arena.length=300, mean.log.individuals=2, 
length.parameter=5000, sd.parameter=50, max.distance=20, proportion.killed=0.2,
competition.iterations=3)

results <- runSimulations(prepped)
# }